rgt-TDF AttributeError: 'Statistics' object has no attribute 'tpx_ndef'

[SophieEhres]

Hello, I was trying to run rgt-TDF and got the following error:

TDF - Regulatory Analysis Toolbox (RGT). Version: 1.0.2

(rgt_env) SAU08:triplex ehresms$ rgt-TDF promotertest -r FENDRR_human_transcripts.fa -de DEG_FENDRR_Names.txt -organism hg38 -rn FENDRR_names -o /Users/ehresms/computational/FENDRR_triplex_promotertest -showdbs

*************** Promoter Test ****************
*** Input RNA sequence: /Users/ehresms/SauvageauLab Dropbox/SauvageauLab/Members/EHRESMANN_Sophie/Projects/FENDRR/triplex/FENDRR_human_transcripts.fa
*** Output directory: computational/FENDRR_triplex_promotertest/FENDRR_names
Step 1: Calculate the triplex forming sites on RNA and DNA.
Dump to file: tdf.dump.hg38.DEG_FENDRR_Names
Running time: 0:04:54
Step 2: Calculate the frequency of DNA binding sites within the promoters.
DEBUG: file_tpx_nde is /Users/ehresms/computational/FENDRR_triplex_promotertest/FENDRR_names/nontarget_promoters.tpx
Counting frequency of promoters on DBD...
620 Binding target promoters
DEBUG: Loaded nontarget_promoters.tpx
34816 Binding non-target promoters
Counting frequency of binding sites on DBD...
620 Binding sites on de promoters
Traceback (most recent call last):
File "/opt/anaconda3/envs/rgt_env/bin/rgt-TDF", line 11, in
sys.exit(main())
File "/opt/anaconda3/envs/rgt_env/lib/python3.7/site-packages/rgt/tdf/Main.py", line 356, in main
file_tpx_de=tpx_de, file_tpx_nde=tpx_nde)
File "/opt/anaconda3/envs/rgt_env/lib/python3.7/site-packages/rgt/tdf/Statistics.py", line 138, in count_frequency_promoters
numdbs_ndef = len(self.tpx_ndef.get_dbs(rm_duplicate=True))
AttributeError: 'Statistics' object has no attribute 'tpx_ndef'

#########

The error in Statistics.py:

  if self.pars.showdbs:
            self.frequency["hits"] = {"de": OrderedDict(), "nde": OrderedDict()}
            numdbs_def = len(self.tpx_def.get_dbs(rm_duplicate=True))
            numdbs_ndef = len(self._tpx_ndef_.get_dbs(rm_duplicate=True))
            for rbs in self.rbss:
                # DE
                l1 = len(self.tpx_def.merged_dict[rbs])
                self.frequency["hits"]["de"][rbs] = [l1, numdbs_def - l1]
                # non-DE
                l2 = len(self._tpx_ndef_.merged_dict[rbs])
                self.frequency["hits"]["nde"][rbs] = [l2, numdbs_ndef - l2]

tpx_ndef should be tpx_nde

thanks!

Sophie